Of course, if Toyota announces any other recalls around this issue in the next year or so, they could really take a big hit. I think they know this and I know the company well enough to be confident they are not dumb enough to be deliberately covering something up. If some new problem surfaces though nobody is going to believe them if they claim no prior knowledge.
I think Toyota will get beyond this, but will suffer along the way. The Audi comparison may not fit as Audi was a much smaller company than Toyota is today. Don't underestimate the power of the Toyota dealers to deal with this and move sales forward.